Locus 3568

Sequence ID 2R_DroMel_CAF1
Location 11,889,766 – 11,889,900
Length 134
Max. P 0.984877
window5810 window5811 window5812 window5813

overview

Window 0

Location 11,889,766 – 11,889,861
Length 95
Sequences 4
Columns 103
Reading direction forward
Mean pairwise identity 92.89
Mean single sequence MFE -40.90
Consensus MFE -32.53
Energy contribution -32.78
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -3.13
Structure conservation index 0.80
SVM decision value 1.15
SVM RNA-class probability 0.922956
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11889766 95 + 20766785
CCGUUGUGUCCACUGGCAUUGGCC--------AUUUGGGCGGUGCUGCUAUUGCUUUUGGCCCCUUUGGUUGGCCAAAUGGCAACUGGCAACGGCUGCUGCGU
.(((.(((.((...(((((((.((--------....)).)))))))((((((((((((((((((...))..))))))).))))).))))...)).))).))). ( -38.90)
>DroSec_CAF1 30259 94 + 1
CCGUUGUGUCCACUGGCAUUGGCC--------AUUUGGGCGGUGCUGCUAUUGCUUUUGGCCCU-UUUGUUGGCCAAAUGGCAACUGGCAACGGCUGCUGCGU
.(((.(((.((...(((((((.((--------....)).)))))))((((((((((((((((..-......))))))).))))).))))...)).))).))). ( -39.30)
>DroSim_CAF1 30416 94 + 1
CCGUUGUGUCCACUGGCAUUGGCC--------AUUUGGGCGGUGCUGCUAUUGCUUUUGGCCCU-UUUGUUGGCCAAAUGGCAACUGGCAACGGCUGCUGCGU
.(((.(((.((...(((((((.((--------....)).)))))))((((((((((((((((..-......))))))).))))).))))...)).))).))). ( -39.30)
>DroEre_CAF1 32209 102 + 1
CCGUUGUGUCCACUGCCAUUGGCCAUUUGGCCAUUUGGGCGGUGCUGGUAUUGCUUUUGGCCCU-UUUGUUGGCCAAAUGGCAACUGGCAACGGCUGUUGCGU
(((((((...(((((((..(((((....)))))....)))))))......((((((((((((..-......))))))).)))))...)))))))......... ( -46.10)
>consensus
CCGUUGUGUCCACUGGCAUUGGCC________AUUUGGGCGGUGCUGCUAUUGCUUUUGGCCCU_UUUGUUGGCCAAAUGGCAACUGGCAACGGCUGCUGCGU
(((((((.......(((((((.((............)).)))))))....((((((((((((.........))))))).)))))...)))))))......... (-32.53 = -32.78 +   0.25)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,889,766 – 11,889,861
Length 95
Sequences 4
Columns 103
Reading direction reverse
Mean pairwise identity 92.89
Mean single sequence MFE -34.15
Consensus MFE -28.22
Energy contribution -27.85
Covariance contribution -0.37
Combinations/Pair 1.04
Mean z-score -3.20
Structure conservation index 0.83
SVM decision value 1.54
SVM RNA-class probability 0.962755
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11889766 95 - 20766785
ACGCAGCAGCCGUUGCCAGUUGCCAUUUGGCCAACCAAAGGGGCCAAAAGCAAUAGCAGCACCGCCCAAAU--------GGCCAAUGCCAGUGGACACAACGG
.........(((((((..(((((..(((((((.........))))))).))))).))))).((((.....(--------(((....)))))))).......)) ( -30.70)
>DroSec_CAF1 30259 94 - 1
ACGCAGCAGCCGUUGCCAGUUGCCAUUUGGCCAACAAA-AGGGCCAAAAGCAAUAGCAGCACCGCCCAAAU--------GGCCAAUGCCAGUGGACACAACGG
.........(((((((..(((((..(((((((......-..))))))).))))).))))).((((.....(--------(((....)))))))).......)) ( -31.50)
>DroSim_CAF1 30416 94 - 1
ACGCAGCAGCCGUUGCCAGUUGCCAUUUGGCCAACAAA-AGGGCCAAAAGCAAUAGCAGCACCGCCCAAAU--------GGCCAAUGCCAGUGGACACAACGG
.........(((((((..(((((..(((((((......-..))))))).))))).))))).((((.....(--------(((....)))))))).......)) ( -31.50)
>DroEre_CAF1 32209 102 - 1
ACGCAACAGCCGUUGCCAGUUGCCAUUUGGCCAACAAA-AGGGCCAAAAGCAAUACCAGCACCGCCCAAAUGGCCAAAUGGCCAAUGGCAGUGGACACAACGG
.((......(((((((((...((((((((((((.....-.((((.....((.......))...))))...))))))))))))...)))))))))......)). ( -42.90)
>consensus
ACGCAGCAGCCGUUGCCAGUUGCCAUUUGGCCAACAAA_AGGGCCAAAAGCAAUAGCAGCACCGCCCAAAU________GGCCAAUGCCAGUGGACACAACGG
.........((((((((((((((..(((((((.........))))))).))))).(((.....(((.............)))...)))...)))...)))))) (-28.22 = -27.85 +  -0.37)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,889,790 – 11,889,900
Length 110
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 96.83
Mean single sequence MFE -43.52
Consensus MFE -42.21
Energy contribution -42.52
Covariance contribution 0.31
Combinations/Pair 1.03
Mean z-score -2.83
Structure conservation index 0.97
SVM decision value 1.99
SVM RNA-class probability 0.984877
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11889790 110 + 20766785
--AUUUGGGCGGUGCUGCUAUUGCUUUUGGCCCCUUUGGUUGGCCAAAUGGCAACUGGCAACGGCUGCUGCGUUGGCCUUGUUAAAUUAUGCUCGUCAUGGCGGCACUUCCG
--.....((.(((((((((((.((....((((.....))))((((((..((((.(((....))).))))...))))))................)).))))))))))).)). ( -45.30)
>DroSec_CAF1 30283 109 + 1
--AUUUGGGCGGUGCUGCUAUUGCUUUUGGCCCU-UUUGUUGGCCAAAUGGCAACUGGCAACGGCUGCUGCGUUGGCCUUGUUAAAUUAUGCUCGUCAUGGCGGCACUUCCG
--.....((.(((((((((((.((....(((...-((((..((((((..((((.(((....))).))))...))))))....))))....))).)).))))))))))).)). ( -44.60)
>DroSim_CAF1 30440 109 + 1
--AUUUGGGCGGUGCUGCUAUUGCUUUUGGCCCU-UUUGUUGGCCAAAUGGCAACUGGCAACGGCUGCUGCGUUGGCCUUGUUAAAUUAUGCUCGUCAUGGCGGCACUUCCG
--.....((.(((((((((((.((....(((...-((((..((((((..((((.(((....))).))))...))))))....))))....))).)).))))))))))).)). ( -44.60)
>DroEre_CAF1 32239 111 + 1
CCAUUUGGGCGGUGCUGGUAUUGCUUUUGGCCCU-UUUGUUGGCCAAAUGGCAACUGGCAACGGCUGUUGCGUUGGCCUUGUUAAAUUAUGCUCGUCAUGGCGGCACUUCCG
.......((.(((((((.((((((((((((((..-......))))))).))))).((((((.(((((......)))))))))))..............)).))))))).)). ( -39.60)
>consensus
__AUUUGGGCGGUGCUGCUAUUGCUUUUGGCCCU_UUUGUUGGCCAAAUGGCAACUGGCAACGGCUGCUGCGUUGGCCUUGUUAAAUUAUGCUCGUCAUGGCGGCACUUCCG
.......((.(((((((((((.((....(((....((((..((((((..((((.(((....))).))))...))))))....))))....))).)).))))))))))).)). (-42.21 = -42.52 +   0.31)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,889,790 – 11,889,900
Length 110
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 96.83
Mean single sequence MFE -33.12
Consensus MFE -31.64
Energy contribution -31.70
Covariance contribution 0.06
Combinations/Pair 1.03
Mean z-score -2.13
Structure conservation index 0.96
SVM decision value 1.19
SVM RNA-class probability 0.928907
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11889790 110 - 20766785
CGGAAGUGCCGCCAUGACGAGCAUAAUUUAACAAGGCCAACGCAGCAGCCGUUGCCAGUUGCCAUUUGGCCAACCAAAGGGGCCAAAAGCAAUAGCAGCACCGCCCAAAU--
.((..((((.((......................(((.(((((....).))))))).(((((..(((((((.........))))))).))))).)).))))..)).....-- ( -33.00)
>DroSec_CAF1 30283 109 - 1
CGGAAGUGCCGCCAUGACGAGCAUAAUUUAACAAGGCCAACGCAGCAGCCGUUGCCAGUUGCCAUUUGGCCAACAAA-AGGGCCAAAAGCAAUAGCAGCACCGCCCAAAU--
.((..((((.((......................(((.(((((....).))))))).(((((..(((((((......-..))))))).))))).)).))))..)).....-- ( -33.80)
>DroSim_CAF1 30440 109 - 1
CGGAAGUGCCGCCAUGACGAGCAUAAUUUAACAAGGCCAACGCAGCAGCCGUUGCCAGUUGCCAUUUGGCCAACAAA-AGGGCCAAAAGCAAUAGCAGCACCGCCCAAAU--
.((..((((.((......................(((.(((((....).))))))).(((((..(((((((......-..))))))).))))).)).))))..)).....-- ( -33.80)
>DroEre_CAF1 32239 111 - 1
CGGAAGUGCCGCCAUGACGAGCAUAAUUUAACAAGGCCAACGCAACAGCCGUUGCCAGUUGCCAUUUGGCCAACAAA-AGGGCCAAAAGCAAUACCAGCACCGCCCAAAUGG
.((..((((((......)).((............(((.((((((((....)))))..)))))).(((((((......-..))))))).)).......))))..))....... ( -31.90)
>consensus
CGGAAGUGCCGCCAUGACGAGCAUAAUUUAACAAGGCCAACGCAGCAGCCGUUGCCAGUUGCCAUUUGGCCAACAAA_AGGGCCAAAAGCAAUAGCAGCACCGCCCAAAU__
.((..((((.((.((.....((............(((.((((((((....)))))..)))))).(((((((.........))))))).)).)).)).))))..))....... (-31.64 = -31.70 +   0.06)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:58:46 2006